Chaos Theory
by StarKnight2.0
Summary: Doctor Eggman broke into a Shield facility and unleashed a vengeful meta human called Shadow, upon an unsuspecting world. It's up to the X-men to stop them but can they stop a mad scientist and the ultimate lifeform. R&R
1. Chapter 1 Infiltration

**(A/N: i hope you enjoyed this. please tell me what you think.)**

Chaos Theory Ch 1

_**21:02**_

_**S.H.E.I.L.D containment facility 3: undisclosed location. **_

"_**Intruder Alert! Intruder Alert! Security breach detected at gate 3"**_ announced a computer voice while a loud alarm was blaring.

Large metal doors started sealing themselves in an attempt to halt the intruder.

The commander of the base walked into the control room, a room with computers wired to every camera and system in the base, manned by a dozen technicians

"What's going on?" he demanded, a technician analyzing reports from all over the facility said "We have a security breach sir" "I know that, but who is it?" he asked the technician "We don't have a visual sir"the technician replied. "Somebody get me a visual, what's the status of the intruder?" asked the commander

"so far he breached gate 3 and is heading to the sublevels" answered the technician the commander paled "Is he heading towards Juggernaut?" the technician shook his head "no, he's heading deeper into the sublevels, into the older basements" "Sir I got a visual of the intruder" announced another technician.

The commander walked over and looked on the monitor, the image was slightly blurred but he saw it was a large bipedal grey and red robot with a large gun turret on its shoulder, the robot was roughly three times the size of the juggernaut "Get General Fury on the phone and deploy the sentinel " he ordered.

Meanwhile in the sublevels of the facility, Doctor Ivo Robotnick, aka Dr. Eggman, piloted his assault bot with ease, tearing through SHEILD's soldiers chuckling "Hahaha, this to easy" after he dispatched the last of the soldiers his robot stomped it's way into the lift.

The elevator descended deeper into the basement. Doctor Eggman was going through his grandfather's old journal and he discovered something intriguing, a top secret military weapon that was said to be the ultimate weapon but was never put into use because they feared it, so they locked it away deep inside a base and deleted all the files on the weapon trying to keep it hidden but Eggman smirked, his grandfather was a brilliant man and he was the one who created the weapon and kept a vague record of it in his journal.

The elevator slowed to a stop, the large robot stomped out and Eggman saw a large metal door blocking his path, he snickered "as if this could stop me" he then punched in an old access code he procured from his grandpa's journal, the door hissed and slid aside with a loud creak from disuse.

Eggman entered the room, which was big enough to store a dozen tanks in the center was a single control console, the robot knelt down and the chest hissed open and out stepped a tall portly man, a bald head, a large red colored mustache and was wearing blue spectacles and a red jacket as well as black pants.

He booted up the old control console and on the screen it said "_**Welcome user, Enter password"**_ "Hm, M-A-R-I-A" he said to himself typing in the password. The screen went blank and the floor behind the computer slid away revealing a wires and pipes and a pod that was almost six feet long, was raised on a platform and was placed in front of Eggman

"Oh ho, so this is the weapon, smaller then I expected" he pulled out a silver jewel that fit perfectly in his palm, from his coat pocket "This Chaos emerald should do the trick" Eggman spotted a keypad on the side of the pod and a port for a Chaos emerald to be placed.

He placed it in the port and the keypad blinked on and he typed in another code and the pod started hissing out smoke, the fogged glass lid opened and a shape sat up from the pod.

Eggman narrowed his eyes at the shape, which seemed familiar and he growled, "Is that you Sonic, are you trying to ruin my plans again you wretched…" but he stopped and saw that it was not his enemy, but someone else.

Out from the pod stepped a boy in his teens; he had black spiky hair with red streaks, he had crimson eyes and he wore a red shirt, a black jacket, dark pants and red and white sneakers. Eggman was surprised and was silent, after a moment of silence Eggman found his voice "Y-your not sonic, who are you?" the teenager noticed Eggman then made a slight bow "My name is Shadow, since you were kind enough to release me, my master I will grant you one wish" Eggman raised an eyebrow and was about to ask Shadow what he meant but the alarm blared and the metal door exploded, revealing squads of soldiers and a sentinel "Stand down now" said the leader.

Eggman studied the sentinel muttering; "So the reports were true, they finally built one" he knew about the sentinels he cursed knowing that the sentinel's armor can withstand his weapons, Shadow put a hand on his shoulder "Allow me" he said in a quiet voice.

Eggman stood aside, Shadow stepped forward "Stand down or we will shoot" ordered the commander Shadow looked over his shoulder "Witness a small sample of my power, master" he turned his attention back to the guards then Shadow became a black and red blur.

Before the soldiers could react, they all were knocked unconscious on the ground, the sentinels sensors tried to keep up but Shadow was to quick, he ran up the sentinel's leg and he pushed off the robot's chest, Shadow spun flicked his wrist and a bolt of golden energy shot out of his hand and struck the sentinel in the chest and pierced its armor leaving a large hole in it's chest, the sentinel collapse with a loud crash.

Shadow landed on the ground and grunted "Pathetic fools" then he bowed to Eggman "I hope you are pleased" Eggman was flabbergasted then said "Shadow that was amazing" Shadow smiled a little then said "We must leave now more SHEILD agents will arrive" Eggman nodded, he climbed back into his mec and Shadow hopped onto the robot's shoulder and the robot lumbered out of the storage room and into the lift.

General Fury inspected the destroyed sentinel "The intruders escaped through the south sector sir, Juggernaut is still in prison and we have sustained minimal casualties" said the base commander.

Fury scratched his chin "Anything taken?" "Uh, well we're not sure sir, any files referring to that pod has been deleted or extremely corrupted to be opened, we are still cross-referencing our database on the robot"

"Anything yet?" asked Fury still inspecting the sentinel "uh no results so far, the design is custom, it's unlike anything anyone has come across before and there are no prints on the key pads"

General Fury grumbled to himself "Some guy in a supped up robot came in, kicked our asses, opened a pod we know little about, five squads and a sentinel intercept then get their asses handed to them" then he told the base commander

"I can't believe I'm saying this but we're going to need Xavier's help" Fury pulled a cigarette out of his mouth, lit it and said "Get this cleaned up" the commander saluted. Fury walked back to the lift grumbling, "This is going to be a long night"

End of Chapter 1

**(A/N: i hoped you enjoyed this. please review)**


	2. Chapter 2 Free Fall

**(A/N: i hope you enjoy. sorry for the wait, tell me what you think of the story in the review)**

Chaos Theory ch 2

_**21: 32**_

_**Xavier school for gifted youngsters, Bayville**_

There was a knock at mansion's front door, the mutant known as Logan growled walking to the door "Who the hell would be knocking at this time of night" he sniffed the air and grumbled something and opened the door revealing General Fury"What the hell do you want Fury?" growled Logan.

Fury smiled a bit "Nice to see you too Logan, I was wondering if the professor is here" "_I am",_ said Xavier telepathically.

Logan led Fury to Xavier's office grumbling something, in his Xavier sat behind his desk "General, what brings you here at this hour?" asked Xavier, Fury sat down in a chair in front of his desk, he said "Bad news"

"With you it's always bad news" hissed Logan "And what has this got to do with us?" Fury sighed, "polite as always Logan, but I think this might concern you, about a half hour ago the facility that the Juggernaut was broken into" Xavier's and Logan's eyes widened in surprise "But the Juggernaut wasn't released, thank god for that but the intruder didn't attempt to hack our computers or steal any of our weapons"

"What was this intruder looking for?" asked Xavier Fury shrugged "hell if I know, we're still working that part out, he broke into the sublevels of the base, which contained a bunch of old research junk that isn't useful to anyone but this intruder finds this pod in the deepest room in the base and security managed to catch up and intercept them with a sentinel" "So what's the problem? The sentinel is a bit of an overkill, Fury" said Logan Fury nodded "I know, it is a bit of an overkill but that's the thing, from the reports I read, the squad was taken down and the sentinel was destroyed in five seconds flat"

Logan and Xavier looked at Fury in surprise "No way that's possible, we threw everything at the first one and it didn't seem fazed" said Logan Fury nodded "That's what I thought but from the security video's that I saw I just couldn't believe it. I'm just as surprised as you" he pulled out a photo from his jacket and placed it on Xavier's desk, it showed a sentinel on the ground with a hole the size of a car in it's chest.

Xavier took a moment to absorb the information "What do you want us to do?" asked Xavier "Well nothing at the moment, but I want you and your students to keep a sharp eye out, for all we know we could be facing an omega class mutant or worse" "Worse?" asked Logan Fury shrugged "With what we deal with the shit could hit the fan faster then anyone could say oops" Fury stood then left.

_**20:22 Egypt: undisclosed location.**_

Eggman's robot lumbered into the hanger, with Shadow on his shoulder.

The robot slowed and knelt down and Eggman stepped out of the robot, Shadow jumped off the robot's shoulder and looked around at the old hanger "I like what you done with the place" said Shadow Eggman walked towards the door at the far side of the hanger "It's not much but it will do" they both went to the control room of the doctors base, the lights switched on automatically, the room was circular in the center was a large flat screen and large key board.

Eggman typed in some commands and the computer blinked on and news reports from all over the world appeared on the screen "Shadow, at the facility you said you would grant me a wish, what exactly do you mean?" asked Eggman crossing his arms

Shadow smiled "I can give you the power to conquer this world" Eggman raised an eyebrow "Oh and how am I to do that?" Shadow typed in some commands in the computer and newspaper articles and pictures of several gems all similar but different colors "The first step is to gather the seven chaos emeralds, they are the key to world domination" Eggman rubbed his chin deep in thought then agreed "Indeed, where do we start?"

Shadow pushed a key on the keyboard and the picture of an emerald colored jewel appeared on the screen "This one is the least guarded and will be easiest to steal" "Where is it stored?" asked Eggman "The museum of natural history in Bayville" answered Shadow "It is being featured in the exhibit of Babylonian myths and legends" Eggman nodded "Good" Shadow typed in some commands into the computer turned and walked to the door

"I programmed coordinates into your computer, meet me at that location in a few hours, I will meet you there with the chaos emerald" Shadow walked out the door and left the base.

Eggman adjusted his glasses and analyzed the coordinates "Hmm, that's strange it just leads to outer orbit, there's absolutely nothing there, I wonder what Shadow is up to," thought Eggman scratching his chin.

_**13:27 above Bayville**_

A SHIELD helicopter flew over the town of Bayville heading towards a SHIELD facility, the sky was clear and the sun shined down on the town. The helicopter transporting at least a dozen guards and a single prisoner, the prisoner took a long time and effort to catch, he was quick, just as quick as the intruder, and he was cleaver.

They manage to trick him using a trap, and now they were dragging him in for questioning,

"This is Sigma-Alpha 2 heading due south over Bayville, We're en route, everything's a go" said the pilot on the radio "This is control, we have you on radar, report cargo status of captured Meta-human" came the reply, "That's a 10-4 cargo is secure on board and…" the pilot didn't finish because he looked behind him and saw all the guards were being knocked out and the prisoner was slamming himself against the door trying to knock it open.

"Sorry didn't catch that, can you repeat" asked Command "The prisoner is taking down everyone aboard" he reported "What's wrong come in over!" demanded Command as the radio died.

The prisoner knocked open the door and he was sucked out by the wind and he caught onto the skids, the wind rushing through his hair.

The Prisoner was a teenager, with dark blue hair; he wore a white shirt, and a blue jacket, jeans, red sneakers and he had a pair of red goggles around his neck.

He kept his name a secret but everyone calls him "Sonic" because he can run faster then the speed of sound.

He held on to dear life mumbling "Talking about low budget flights, no movies or food, I'm out of here" he pulled himself up and pulled off a loose metal panel from inside the helicopter, he put his goggles on stepping onto the metal panel

"What the hell are you doing?" exclaimed the pilot Sonic just grinned and gave him a thumbs up "Thanks for the ride, this is my stop" he then pushed himself out the door, using the panel as a board he was dropping out of the sky, he spun yelling at the top of his lungs "Yahoo!" falling out of the sky at accelerating rate.

End of chapter 2

**(A/N: i hope you liked this. review and leave some ideas if you have any.)**


	3. Chapter 3 Arrested Development

**(a/n: wow sorry for the delay, its been hectic and i sort of lost interest but now i'm back to writing this story again! now i'll be changing things a little like writing the times and locations. i'll keep the locations but not the times. anyway enjoy)**

Chaos Theory Ch 3

**13:29, 2 miles outside Bayville, New York**

Sonic held onto the makeshift board, wind rushing through his hair, he spun a few more times doing some flips and other tricks; he landed into the harbor with a splash.

Sonic got out of the water quickly and dried himself off he hated swimming. He sat on the ground thinking about what had happened to him lately, one minute he was at home eating a chili dog and the next thing he knew he was being chased by government agents then dragged off into a helicopter that was flying to, who knows where to do, who knows what.

Sonic stood up and he started walking away from the harbor

"I wonder if there's any chili dog's around?" asked Sonic to no one in particular.

The sound of sirens came closer to the harbor and the next thing Sonic knew police cars and black SUV's surrounded him.

Police officers got out of their cars and aimed their guns at him "Don't move!" yelled one officer,

Sonic groaned "I just can't catch a break can I?" then he ran, turning into a blue and red blur he bypassed the cops, passed a bunch of warehouses and took off running down the road towards Bayville with the police hot on his heels.

**13:30, Bayville High, Bayville, New York**

A yellow bus was parked in front of the high school, students were standing single file next to the bus boarding the vehicle, and their teacher was checking attendance as the students boarded the bus. All of a sudden a blue blur passed by the school and bus in a blink of an eye, kicking up dust and a breeze then about fifteen minuets later, a bunch of police cars and black SUV's drove pass quickly and disappeared in the distance.

A red haired girl and a guy with dark sunglasses looked out the window towards where the cars were headed "What was that all about?" asked Jean Grey to Scott Summers, he shrugged "I don't know but whatever that was it's not normal"

"do you think it could be a mutant?" asked Jean Scott scratched his chin "Maybe, we should ask the professor later" the last of the students got on to the bus, the teacher followed suit and he announced "Alright everyone be on their best behavior, remember not pushing, shoving or arguing. Don't forget, do not to touch the exhibits in the museum" he looked around at the students and then sat down, the bus's engine grumbled and then the bus pulled out and drove to the museum.

_**Five minutes later, Bayville Museum of Natural History **_

The bus slowed and stopped in front of the museum, the teacher and the students got off the bus and went inside.

The main lobby had a banner announcing the new Babylonian exhibit.

The class toured through the museum's exhibit of various artifacts till they reached a single room. It had a single glass case that had an emerald jewel that was the size of a baseball and beside it was a small stone tablet "Wow, what is that" asked a girl named Kitty "That is a Chaos Emerald" answered an old sounding voice.

Everyone turned and saw an old man in dark clothes and a teenager with red hair; they walked over to the group

"What's a Chaos Emerald?" asked Scott

the old man blinked "You don't know what a Chaos Emerald is? Jeez what do they teach you kids in school" "probably nothing gramps" snorted the red head.

The old man scratched his chin "Well not much is known about the Chaos Emerald like where they come from and who made them but legend says that there were seven emeralds and if they were brought together they could make a miracle happen"

"What kind of miracle?" asked Jean

the old man shrugged "heal people, grant a wish Hell if I know, it's just a story. My grandson and I had this little thing for years and we haven't had a miracle at all" The old man smacked himself on the forehead "Where are my manners I'm Miles and this is my grandson Kyle" "call me Knuckles" grunted the red head.

Duncan snorted "That's a dumb name" Knuckles glared at Duncan snarling then there was a crash and an explosion causing the ceiling the collapsed revealing a large floating vehicle containing a single passenger.

Knuckles eyes widened and he grinned "Eggman" the man had a large mustache and wore red he grinned, "Well, well, well if it isn't little Knucklehead"

"Back for another round of ass kicking? Or have you just invent something that can kick you're ass for you" everyone stayed still while some ran out of the room "Who are you?" asked Scott.

Eggman tilted his head "My name is Robotnick the worlds greatest scientific mind, now if you excuse me I got personal business to attend to" he snapped his finger and a bunch of gold shapes appeared in a flash of light and everyone saw they were robotic wasps. All the students except Scott, Jean and Kitty left the room.

Knuckles turned to his grandfather "You might want to sit this out pops" Miles waved "Oh sure don't mind me" he walked out of the room saying, "If you need me I'll be at the gift shop".

Scott shot at most of the wasps with his optic blasts, Jean caused a few to crash into each other and Knuckles saw that a Eggman had the emerald in his hand "He's getting away!" exclaimed Jean.

Knuckles grunted "not if I can help it" he clenched his fists, two spikes popped out of his knuckles, he crouched and jumped into the air as Eggman ascended "Wha-" exclaimed Eggman as Knuckles punched a hole in Eggman's vehicle causing it to drop a little and the emerald slipped out of Eggman's grip. Knuckles caught it, back flipped and he landed on the ground. Eggman regained control of his hovercraft and it started ascending again "Ha I win!" shouted Knuckles

Eggman grinned "Oh really, not this time Knucklehead!" he snapped his fingers again, a black and red blur dropped down from the destroyed roof, zoomed around Knuckles and landed on Eggman's hovercraft, Knuckles looked at his hands and saw that the emerald was gone, he looked up and saw Eggman holding it. Sitting on the edge of the hovercraft was a teen dressed in black and he had black spiky hair with streaks of red "Sonic?" breathed Knuckles then Eggman zoomed out of the destroyed roof.

Knuckles's spikes retracted into his hands, he glared up at the hole in the ceiling "You're a mutant?" said Scott

Knuckles shrugged "I guess, not a big deal really"

"who was that?" asked Jean

"Dr. Robotnick, or Eggman as I call him, a brilliant man but he's a twisted criminal bent on taking over the world" said Knuckles.

Knuckles shoved his hands in his pockets "Well its been a blast but I'm out of here, I got to stop Eggman" he began walking out of the room "Hey wait up" called Kitty "You're going to stop him?"

Knuckles shrugged "yeah I've done it dozens of times" "alone?" "Yeah, well sometimes I got help but I'm fine on my own" said Knuckles "We can help" said Jean.

Knuckles shook his head "No can do, I can handle that Egg myself. Besides I'm the guardian of the chaos emeralds, its my job to protect them and I don't want anybody getting in my way" before the three mutants could talk to him he left.

Scott looked at Jean and said "Two mutants and a crazy scientist in one day, I think we should tell the Professor, he might know what to do" Jean nodded and the three of them left quickly before security arrived.

Night had fallen over Bayville and Sonic had lost the police and SHIELD agents. Sonic sat down on a park bench to catch his breath until his cell phone rang, he picked it up "hello?"

"Hey Sonic!" said a familiar voice

"Knuckles, man its good to hear you're voice" said Sonic sounding relieved "You got to help me"

"I was going to ask you the same thing" said Knuckles "Were you by any chance at the Museum of natural history?"

"No, I've been chased around by guys in vans all day, why?" "You don't have a twin do you?" "No why do you-" but Sonic stopped as he saw someone who looked almost exactly like him appear in the park in a blur of black and red.

Sonic heard Knuckles retell a story about Eggman robbing the museum of the chaos emerald and was with someone who looked like him.

Sonic stood up "Knuckles I think I found you're thief" said Sonic "If you don't hear from me in the next few hours, get Tails and try to get those emeralds back from Eggman" "Alright but what are you-" then Sonic hung up and shoved his phone back in his pocket.

Sonic walked over to the duplicate and he heard him say triumphantly "It all starts with this" he held up a green chaos emerald aloft, it shone in the moonlight "A jewel containing the ultimate power!" "I found you!" said Sonic "You're the one who robbed the museum and those suits must have been looking for you!"

The duplicate just stood there staring at Sonic.

Sonic growled and he charged at the imposter at full speed "Say something you imposter!" suddenly the imposter disappeared in a blur of black and red.

Sonic saw him dart past him at an equally high speed; Sonic skidded to a stop "Wow he's fast" he muttered to himself.

Suddenly the imposter disappeared from his view and he reappered on top of a lamp post, holding aloft the chaos emerald

"My name is Shadow" said the imposter "I'm the world's ultimate life form, I would love to play with you but for now I have no time to play games, farewell" he tossed the emerald in the air and caught it and he vanished in a flash of green light.

Sonic shielded his eyes, he relized that he could use the chaos emerald to make himself faster then suddenly he heard a bunch of car screeches

"What the?" Sonic looked around and saw that he was surrounded by SWAT, Police and men in suits all aiming weapons at him "Don't move!" screamed one of the men

"Oh come on!" whined Sonic as he was tackled to the ground by a group of police men and was cuffed. A news van stopped and a camera crew quickly got out and tapped the whole thing, Sonic struggled and was babbling about his rights. The police men tossed him into the back of a truck and the truck zoomed away. From a distant rooftop Shadow watched in amusement "I'll be seeing you around" he muttered and he vanished in a flash of light.

End of chapter.

**(a/n: well there you go. review!)**


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